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Diversity of Microorganisms Within Rock Varnish in the Whipple Mountains, California† K

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Diversity of Microorganisms Within Rock Varnish in the Whipple Mountains, California† K APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Feb. 2006, p. 1708–1715 Vol. 72, No. 2 0099-2240/06/$08.00ϩ0 doi:10.1128/AEM.72.2.1708–1715.2006 Copyright © 2006, American Society for Microbiology. All Rights Reserved. Diversity of Microorganisms within Rock Varnish in the Whipple Mountains, California† K. R. Kuhlman,1* W. G. Fusco,2 M. T. La Duc,1 L. B. Allenbach,2 C. L. Ball,2 G. M. Kuhlman,1 R. C. Anderson,1 I. K. Erickson,3 T. Stuecker,1 J. Benardini,2 J. L. Strap,2 and R. L. Crawford2 Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 911091; Environmental Biotechnology Institute, University of Idaho, Moscow, Idaho 83844-10522; and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844-30513 Received 16 February 2005/Accepted 19 October 2005 Rock varnish from Arizona’s Whipple Mountains harbors a microbial community containing about 108 microorganisms g؊1 of varnish. Analyses of varnish phospholipid fatty acids and rRNA gene libraries reveal a community comprised of mostly Proteobacteria but also including Actinobacteria, eukaryota, and a few members of the Archaea. Rock varnish represents a significant niche for microbial colonization. Rock varnish (also known as desert varnish) is a dark, thin forms very slowly at rates thought to be between Ͻ1 to about (usually 5 to 500 ␮m thick), layered veneer composed of clay 40 ␮m per 1,000 years (50), thus archeologists have been in- minerals cemented together by oxides and hydroxides of man- terested in dating the age of varnishes to place petroglyphs ganese and iron (11, 20, 56, 63, 64). Nineteenth century refer- etched into varnish by ancient cultures into their full historical ences to rock varnish include those of Humboldt (42) and context (22, 90). Unfortunately, radiocarbon dating of varnish Darwin (14). Modern observations of varnish were initiated has proven difficult, and results must be used with caution (7, with the studies of Laudermilk (49) and Engel and Sharp (25); 9, 17, 22, 62). however, despite decades of study, the nucleation and growth It has been suggested that varnish or varnish-like materials mechanisms of rock varnish remain a mystery (11, 18, 37, 44, may exist on Mars (2, 36, 44, 65). If so, varnish may be a niche 57, 58). for colonization by extraterrestrial life forms such as bacteria. Mn(II) is the soluble form of manganese that is available to Microorganisms are ubiquitous within varnishes on Earth. organisms. It is stable between pH 6 and 9. Mn(III) and Thus, the study of Earthly varnishes may lead to the proper Mn(IV) primarily form insoluble oxides and oxyhydroxides. design of experiments in coming decades for detection of life Microbial Mn(II) oxidation could thus result in the formation on other planets. For example, iron and manganese oxidation of manganese oxides as mineral phases in varnishes, as occurs by microbes cultivated from varnish has been extensively in- in other environments (23, 39). Like manganese oxidation, iron vestigated (1, 19, 26, 33, 43, 46, 47, 54, 56, 77, 78, 80, 83). Perry oxidation (95) occurs at the exterior of the cell surface. Iron et al. (59) observed a variety of amino acids in rock varnish and hydroxides are often deposited on the remains of biogenic suggested that this is evidence for an intimate association of structures (24). The extracellular deposition of ferric hydrox- bacteria with the varnish material. A large variety of bacterial ides is a way for iron-oxidizing organisms to prevent encrusta- genera have been cultivated from rock varnish. These include tion in iron oxide precipitates (88). Such precipitates might be Bacillus (43, 56), Geodermatophilus, Arthrobacter, Micrococcus, incorporated in a varnish matrix through the activities of iron- Curtobacterium, Cellulomonas (43, 48), Pedomicrobium, and a oxidizing bacteria. Metallogenium-like strain (19, 20). Eppard et al. (26) isolated Rock varnish may hold a record of the microclimate in which several actinomycete species including Geodermatophilus. Sta- it is found (7, 10, 11, 30), a hypothesis that has been questioned ley et al. (78, 79) observed microcolonial fungi on rock varnish. previously (67, 68). Some investigators suggest that rock var- nish may harbor a historical record of important environmen- Taylor-George et al. (83), Gorbushina et al. (32), and Perry tal processes such as long-term climate change (51). Bao et al. (55) have provided evidence that these fungi may be involved (7) studied preservation of atmospheric signatures in rock var- in the formation of varnish. nish and concluded that rock varnishes or other surface depos- To our knowledge, only two studies to date have investigated its may provide a record of paleoclimatic information and the microbial phylogenetics of varnish (26, 57). Eppard et al. sulfur biogeochemical cycles. As a deposit of submicrometer (26) used 16S rRNA gene sequencing techniques to examine layering, rock varnish may record the activity of dust storms, phylotypic characteristics of bacteria that had previously been moisture and temperature fluctuations, biological activity, and cultured from various rock varnishes. Kuhlman et al. (48) em- the occurrence of fires over thousands of years. Rock varnish ployed 16S rRNA gene sequencing to identify several UV light-resistant bacteria isolated from rock varnish obtained in the Whipple Mountains of the U.S. Mojave Desert. These * Corresponding author. Present address: Planetary Science Insti- strains included representatives of the genera Geodermatophi- tute, 1700 East Fort Lowell Rd., Suite 106, Tucson, AZ 85719. Phone: lus, Arthrobacter, Curtobacterium, and Cellulomonas. There are (520) 622-6300. Fax: (520) 622-8060. E-mail: [email protected]. † Supplemental material for this article may be found at http://aem several reports of “microcolonial” fungi living within rock var- .asm.org/. nish or on the surfaces of rocks in hot, dry deserts (45, 55, 56, 1708 VOL. 72, 2006 DIVERSITY OF MICROORGANISMS WITHIN ROCK VARNISH 1709 78, 79, 83). The first scanning electron microscope images of homogeneous, and incubated at room temperature for 30 min. such microcolonial fungi were reported from samples collected The samples were stained with 60 ␮lmlϪ1 of a stock 4Ј,6Ј- in the Sonoran Desert in 1978 (55). The fungi observed were diamidino-2-phenylindole (DAPI) or acridine orange (50 ␮g thought to be representatives of the ascomycetes. It has been mlϪ1) solution. DAPI-stained samples were incubated at room suggested that these fungi are the predominant biological temperature for 30 min in the dark before filtration. The most forms observed on rock varnish coatings (32, 55, 60, 79, 80) and appropriate volume for analysis was determined to be 500 ␮lof may be involved in the formation of varnish (83). the 10Ϫ3 dilution. This dilution contained Ͼ25 but Ͻ250 cells Most organisms in nature are refractory to cultivation (4, 8, per field and had a low enough mineral content to both count 85, 89); therefore, many organisms that occupy the varnish cells in about one microscopic plane and not have cells ob- habitat remain to be discovered. We report here the charac- scured by the varnish minerals. Samples were filtered onto terization of microbial rock varnish communities from the 25-mm Millipore Isopore 0.22-␮m pore-size black polycarbon- Whipple Mountains of the American Sonoran Desert via prep- ate filters (Millipore, Billerica, Mass.) with Whatman 25-mm aration of 16S and 18S rRNA gene clone libraries. These GF/F filters used for support. Fluorescing cells were counted analyses are leading us to a greater understanding of the mi- on a Zeiss Research epifluorescence microscope equipped crobial diversity within these communities and their relevance with an Osram xenon short arc photo optic lamp XBO 75W to the possible occurrence of microbial life on other planets, and Chroma no. 31000 filter set for DAPI/Hoechst/AMCA such as Mars, where life forms face exposure to high fluxes of (Zeiss, Inc., Thornwood, N.Y.). The mean number of fields damaging UV light (13) and extremes of temperature and counted per sample (n ϭ 15) was 57.16. The standard deviation desiccation, such as are seen in locations on Earth where rock per sample was 7.48 fields. The average DAPI direct count of varnishes form. Microorganisms such as those that live or sur- the rock varnish was 9.0 ϫ 107 cells gϪ1 (standard deviation ϭ vive in varnish may also be potential forward contaminants on 1.2 ϫ 107). There was no difference between DAPI and acri- spacecraft structures (73). dine orange direct counts. Varnish samples were collected from alluvial fan deposits PLFA analyses were carried out by Microbial Insights, Inc. surrounding the Whipple Mountains, California. The Whipple (Rockford, Tenn.). Total lipids were extracted (91) and the Mountains lie west of Parker, Arizona, along the eastern polar lipids separated by column chromatography (35). The boundary of the Mojave Desert. Previous studies conducted at polar lipid fatty acids were derivatized to fatty acid methyl the site demonstrated relatively thick varnishes (5 to 100 ␮m esters, which were quantified using gas chromatography (69). thick) on various rock types (5). Varnished rocks and sur- Fatty acid chemical structures were verified by chromatogra- rounding soil samples were collected in February 2003 when phy/mass spectrometry and equivalent chain length analysis. the ground was still wet from winter rains. Only clasts with PLFA are essential components of the membranes of all cells thick coatings (greater than 50 ␮m) on relatively large, flat except those of the Archaea, so their profiles allow for exam- surfaces were collected. It was critical that the samples be ination of most of the important members of many microbial collected as aseptically as possible. Sample purity can never be communities. Since phospholipids break down rapidly upon completely verified, since it is very difficult to characterize cell death in environments examined thus far (91, 92), PLFA contamination associated with local wildlife.
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